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- PDB-6ayg: Human Apo-TRPML3 channel at pH 4.8 -

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Basic information

Database: PDB / ID: 6ayg
TitleHuman Apo-TRPML3 channel at pH 4.8
KeywordsTRANSPORT PROTEIN / ion channel / TRP channel / lysosomal
Function / homologyTRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / NAADP-sensitive calcium-release channel activity / inner ear auditory receptor cell differentiation / autophagosome membrane / late endosome membrane / calcium channel activity / calcium ion transmembrane transport ...TRP channels / Polycystin cation channel / Mucolipin / Polycystin cation channel, PKD1/PKD2 / NAADP-sensitive calcium-release channel activity / inner ear auditory receptor cell differentiation / autophagosome membrane / late endosome membrane / calcium channel activity / calcium ion transmembrane transport / locomotory behavior / lysosomal membrane / early endosome membrane / lipid binding / integral component of membrane / plasma membrane / Mucolipin-3
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.65 Å resolution
AuthorsZhou, X. / Li, M. / Su, D. / Jia, Q. / Li, H. / Li, X. / Yang, J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states.
Authors: Xiaoyuan Zhou / Minghui Li / Deyuan Su / Qi Jia / Huan Li / Xueming Li / Jian Yang
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 8, 2017 / Release: Nov 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 8, 2017Structure modelrepositoryInitial release
1.1Nov 22, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Dec 6, 2017Structure modelAuthor supporting evidencepdbx_audit_support_pdbx_audit_support.funding_organization
1.3Dec 20, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

Structure visualization

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Deposited unit
A: Mucolipin-3
B: Mucolipin-3
C: Mucolipin-3
D: Mucolipin-3

Theoretical massNumber of molelcules
Total (without water)258,5034

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)16780
ΔGint (kcal/M)-162
Surface area (Å2)96880


#1: Protein/peptide
Mucolipin-3 / Transient receptor potential channel mucolipin 3 / TRPML3

Mass: 64625.785 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: MCOLN3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8TDD5

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: human TRPML3 channel at pH 4.8 / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionDetails: TRPML3 was purified in HEPES buffer pH 7.4. Sodium acetate pH 4.6 was added before freezing, which made the pH to be 4.8
pH: 4.8
Buffer component
IDConc.NameFormulaBuffer ID
118 mMHEPESC8H18N2O4S1
2135 mMsodium chlorideNaCl1
30.45 mMLauryl Maltose Neopentyl GlycolC47H88O221
4100 mMsodium acetateCH3COONa1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil holey carbon grid R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 kelvins

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 7676 / Height: 7420 / Movie frames/image: 32 / Used frames/image: 1-32


EM software
1RELION1.4particle selectionto automatically pick particles
2EMAN2particle selectionto semi-automatically pick particles
3Etas1.0image acquisition
5CTFFIND3CTF correction
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
14RELION1.43D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C4
3D reconstructionResolution: 4.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42559 / Symmetry type: POINT
Atomic model buildingRef protocol: AB INITIO MODEL / Ref space: RECIPROCAL

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